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- PDB-4wcg: The binding mode of Cyprinid Herpesvirus3 ORF112-Zalpha to Z-DNA -

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Basic information

Entry
Database: PDB / ID: 4wcg
TitleThe binding mode of Cyprinid Herpesvirus3 ORF112-Zalpha to Z-DNA
Components
  • DNA (5'-D(P*CP*GP*CP*GP*CP*G)-3')
  • ORF112
KeywordsDNA BINDING PROTEIN / Zalpha / Z-DNA / innate immunity / Herpes virus
Function / homology
Function and homology information


double-stranded RNA adenosine deaminase activity / RNA binding
Similarity search - Function
Z-binding domain profile. / Z-binding domain / Adenosine deaminase z-alpha domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Uncharacterized protein
Similarity search - Component
Biological speciesCyprinid herpesvirus 3
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsKus, K. / Athanasiadis, A.
Funding support Portugal, 2items
OrganizationGrant numberCountry
Foundation for Science and Technology (FCT)SFRH/BD/51626/2011 Portugal
Foundation for Science and Technology (FCT)PTDC/BIA-PRO/112962/2009 Portugal
CitationJournal: J.Biol.Chem. / Year: 2015
Title: The Structure of the Cyprinid herpesvirus 3 ORF112-Z alpha Z-DNA Complex Reveals a Mechanism of Nucleic Acids Recognition Conserved with E3L, a Poxvirus Inhibitor of Interferon Response.
Authors: Kus, K. / Rakus, K. / Boutier, M. / Tsigkri, T. / Gabriel, L. / Vanderplasschen, A. / Athanasiadis, A.
History
DepositionSep 4, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORF112
B: ORF112
C: DNA (5'-D(P*CP*GP*CP*GP*CP*G)-3')
D: DNA (5'-D(P*CP*GP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5848
Polymers33,2004
Non-polymers3844
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-70 kcal/mol
Surface area8350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.821, 44.821, 140.082
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein ORF112


Mass: 10775.282 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyprinid herpesvirus 3 / Gene: KHVJ122 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4FTK7
#2: DNA chain DNA (5'-D(P*CP*GP*CP*GP*CP*G)-3')


Mass: 5824.724 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.52 % / Description: hexagonal
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 0.9 M Lithium sulfate , 0.1 M HEPES pH 7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 29, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.5→46.694 Å / Num. all: 27020 / Num. obs: 27020 / % possible obs: 99.7 % / Redundancy: 7.1 % / Biso Wilson estimate: 22.53 Å2 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.015 / Rrim(I) all: 0.04 / Rsym value: 0.037 / Net I/av σ(I): 9.824 / Net I/σ(I): 22.3 / Num. measured all: 191744
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.5-1.587.30.6712.92812938690.260.6712.999.8
1.58-1.686.90.3742.12515936360.1490.374599.9
1.68-1.797.40.2013.82589634960.0780.201999.9
1.79-1.947.10.1216.22283232250.0480.12113.499.9
1.94-2.127.30.07210.12167529850.0280.07220.999.8
2.12-2.377.30.04814.72007527380.0190.04830.999.8
2.37-2.7470.03618.51682823890.0140.03639.399.6
2.74-3.357.10.0320.11454120620.0120.0350.799.2
3.35-4.746.60.02524.21078616420.010.02559.499
4.74-46.69460.02620.558239780.0110.02655.898.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.85 Å46.69 Å
Translation2.85 Å46.69 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.21data scaling
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.15data extraction
PHASER2.5.5phasing
XSCALEdata scaling
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HOB

4hob


Resolution: 1.5→46.694 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2067 1306 4.84 %Random Selection
Rwork0.1776 25654 --
obs0.179 26960 99.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.77 Å2 / Biso mean: 29.5903 Å2 / Biso min: 14.57 Å2
Refinement stepCycle: final / Resolution: 1.5→46.694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms978 246 20 120 1364
Biso mean--62.85 36.37 -
Num. residues----134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091338
X-RAY DIFFRACTIONf_angle_d1.051856
X-RAY DIFFRACTIONf_chiral_restr0.055195
X-RAY DIFFRACTIONf_plane_restr0.005198
X-RAY DIFFRACTIONf_dihedral_angle_d17.224516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.56010.29991400.23652783X-RAY DIFFRACTION100
1.5601-1.63110.30491520.21872786X-RAY DIFFRACTION100
1.6311-1.71710.2111610.18032812X-RAY DIFFRACTION100
1.7171-1.82470.2281480.17112789X-RAY DIFFRACTION100
1.8247-1.96560.19891590.17452811X-RAY DIFFRACTION100
1.9656-2.16340.23751270.17922881X-RAY DIFFRACTION100
2.1634-2.47640.22261530.17472842X-RAY DIFFRACTION100
2.4764-3.11990.235900.1922942X-RAY DIFFRACTION99
3.1199-46.71660.18021760.16663008X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.46384.1631-1.45056.9809-1.97535.6105-0.12080.36920.3036-0.23850.15280.22120.0714-0.2639-0.10420.21580.0573-0.01340.18780.01360.1512-24.489814.8638-18.9223
23.8464-2.2546-0.4715.38740.21137.18020.0282-0.08950.20050.20920.01710.1979-0.3202-0.1596-0.02660.17650.02650.00180.14730.00870.1385-21.998814.7418-11.896
35.55133.56730.45747.89750.13927.23220.08910.324-0.33460.0204-0.0337-0.67340.11420.8176-0.06610.19380.0412-0.00450.2579-0.00780.2008-13.767610.3016-18.1874
41.5647-0.41472.41425.48882.21666.1650.04010.0175-0.0576-0.14320.0551-0.01630.09910.2582-0.08780.25510.01130.00920.1611-0.01140.1479-14.038313.2387-3.6222
54.58210.8644-1.95623.08490.08350.905-0.0631-1.35280.12930.40770.38621.223-1.26940.0924-0.23420.48180.0430.09890.2917-0.06140.4008-25.04567.12260.3383
66.69461.5542-1.12078.09083.82448.59470.0559-0.531-0.2630.0321-0.2162-0.77550.35440.77740.12520.25380.08740.00520.26410.0590.2695-5.6987-6.842-11.6158
75.8645-1.13993.85633.3384-1.07212.8210.0275-0.001-0.4060.0833-0.0684-0.11140.97270.22850.00460.39060.06310.04310.2125-0.00140.3277-13.3523-13.4562-9.1721
85.0652-1.3196-0.86115.5502-1.12559.3083-0.0724-0.24760.16050.08530.0271-0.3196-0.02670.3970.00510.18840.0334-0.00460.144-0.02320.1859-12.828-1.6401-10.2857
93.9080.34420.50845.67670.05526.11270.07260.04370.3217-0.1409-0.01330.27780.1444-0.54540.01420.23010.0259-0.00650.2098-0.02750.1814-20.3703-5.9813-16.8257
105.6845-1.3502-3.35195.7669-1.70515.42830.09520.05340.26830.0296-0.067-0.0589-0.0225-0.0814-0.0340.18860.00710.01230.13520.01360.1249-23.1437-3.2643-3.4086
115.5358-5.2024.59386.506-4.4824.4269-0.1923-1.11940.47930.50290.2624-1.05260.994-0.5038-0.10530.45690.0207-0.09490.2318-0.03110.3231-13.93854.16072.694
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 217 through 237 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 238 through 262 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 263 through 277 )A0
4X-RAY DIFFRACTION4chain 'C' and (resid 5 through 9 )C0
5X-RAY DIFFRACTION5chain 'C' and (resid 10 through 10 )C0
6X-RAY DIFFRACTION6chain 'B' and (resid 217 through 232 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 233 through 248 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 249 through 266 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 267 through 277 )B0
10X-RAY DIFFRACTION10chain 'D' and (resid 5 through 9 )D0
11X-RAY DIFFRACTION11chain 'D' and (resid 10 through 10 )D0

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